Nanopore-based full-length transcriptome sequencing of Muscovy duck (Cairina moschata) ovary

Abstract

Unlike mammals, studies on mechanisms that regulate waterfowl ovulation have been rarely reported. To advance our understanding of the ovulation differences in Muscovy duck, we utilized the Oxford Nanopore Technologies ( ONT ) to generate transcriptome data from 3 groups of female duck ovaries with ovulation differences (i.e., preovulation [ PO] , consecutive ovulation [ CO ], and inconsecutive ovulation [ IO ]). In this study, the full-length transcriptome data qualitative analysis showed that a total of 24,504 nonredundant full-length transcripts were generated, 19,060 new transcripts were discovered and 14,848 novel transcripts were successfully annotated. For the quantitative analysis, differentially expressed genes ( DEGs ) between the 3 groups were identified and functional properties were characterized. CTNNB1, IGF1, FOXO3, HSPA2, PTEN and SMC4 may be potential hub genes that regulate ovulation. Adhesion-related pathway, mTOR pathway, TGF-β signaling pathway and FoxO signaling pathway have been considered as important pathways that affect follicular development and ovulation. These results provide a more complete data source of full-length transcriptome for the further study of gene expression and genetics in Muscovy duck. The hub genes and potential mechanisms that affect the ovulation of Muscovy duck have been screened out to provide a scientific basis for breeding work to improve the reproduction performance of Muscovy duck.

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

“…Using RNA-seq short reads to correct the low-quality isoforms generated by ICE proofread, and then combined the corrected low-quality isoforms and high quality isoforms into the full-length isoforms. In ISO-seq analysis, multiple different isoforms may be generated from the same transcript, and these may also be assigned to different libraries, using TOFU software ( https://github.com/PacificBiosciences/cDNA_primer/wiki/What-is-pbtranscript-tofu%3F-Do-I-need-it%3F ) to remove the redundant isoforms [ 41 ]. Finally, sequences with a coverage less than 0.85 and identity less than 0.9 were filtered, merged only the 5'-end exon with the difference in alignment, and obtained 24,658 non-redundant transcript sequences.…”

Discovering Novel Genes in Non-Model Fly Accessory Glands Using De Novo Nanopore Transcriptomics

“…So far, ONT long-read transcriptomics has been used with one other species that did not have a species-speci c reference database available (the Muscovy duck). However, in that study, the authors used a reference database from a different genus, and characterized well-established and conserved genes (Lin et al, 2021). In contrast, our genes of interest are rapidly evolving, often species-speci c genes from AG of males insects, and we successfully discover more than two dozen novel genes that are found only in S. punctum (Figure 4b).…”

“…However, in non-model species without reference databases, the uptake of ONT long-read transcriptomics has been negligible and there are no studies comparing ONT transcriptomics with other sequencing platforms (e.g., Illumina, PacBio). In fact, a search for ONT transcriptomics of lesser-studied species led us to just one publication on the Muscovy duck where a database from an alternate duck species was used as a reference (Lin et al, 2021) (search conducted on 8th September 2021). The combination of lack of reference databases and high sequencing error rates, makes it especially challenging to undertake de novo ONT transcriptomics (Sahlin et al, 2021;Sahlin & Medvedev, 2019).…”

Integrated ONT Full-Length Transcriptome and Metabolism Reveal the Mechanism Affecting Ovulation in Muscovy Duck (Cairina moschata)

“…In order to track the change process of the metabolome more deeply, we join the transcriptome for multi-omics joint analysis. Previous transcriptomics data showed that a total of 3,046 DEGs (1,046 up-regulated and 2,000 down-regulated) were identified in the PO compared with the CO group (18). A comprehensive analysis of metabolomics and transcriptomics was performed, and 55 Co-enriched pathways were derived (Figure 4), the lipid metabolism-related pathways were dramatically changed, of which we focused on three pathways including Arachidonic Acid metabolism, Glycerophospholipid metabolism and Steroid hormone biosynthesis pathways.…”